Functional genomics of a symbiotic community : shared traits in the olive fruit fly gut microbiota

The olive fruit fly Bactrocera oleae is a major pest of olives worldwide and houses a specialized gut microbiota dominated by the obligate symbiont “Candidatus Erwinia dacicola”. Ca. E. dacicola is thought to supplement dietary nitrogen to the host, with only indirect evidence for this hypothesis so far. Here, we sought to investigate the contribution of the symbiosis to insect fitness and explore the ecology of the insect gut. For this purpose, we examined the composition of bacterial communities associated with Cretan olive fruit fly populations, and inspected several genomes and one transcriptome assembly. We identified, and reconstructed the genome of, a novel component of the gut microbiota, Tatumella sp. TA1, which is stably associated with Mediterranean olive fruit fly populations. We also reconstructed a number of pathways related to nitrogen assimilation and interactions with the host. The results show that, despite variation in taxa composition of the gut microbial community, core functions related to the symbiosis are maintained. Functional redundancy between different microbial taxa was observed for genes involved in urea hydrolysis. The latter is encoded in the obligate symbiont genome by a conserved urease operon, likely acquired by horizontal gene transfer, based on phylogenetic evidence. A potential underlying mechanism is the action of mobile elements, especially abundant in the Ca. E. dacicola genome. This finding, along with the identification, in the studied genomes, of extracellular surface structure components that may mediate interactions within the gut community, suggest that ongoing and past genetic exchanges between microbes may have shaped the symbiosis

Track Structure and the Quality Factor for Space Radiation Cancer Risk

A major risk from exposure to space radiation is the induction of cancer and it is from estimates of this risk that the maximum career flight times of NASA space crew members are restricted by a permissible exposure limit. For the purpose of demonstrating compliance with the career limit, NASA has developed a cancer risk projection model for exposure-induced fatal cancer, in which the formulation and numerical values of the quality factor (QFNASA) are substantially different from those of the quality factor (Q) or radiation weighting factor (wR) routinely applied for radiation protection on earth. The quality factor is used to account for the increased effectiveness of radiations of high linear energy transfer (LET), compared to the effectiveness of low-LET -rays derived from epidemiological studies of the atomic-bomb survivors. The need for a special approach for space radiation is dictated by the special characteristics of the charged particles from solar radiation and especially the charged particles of high energy and charge (HZE) in galactic cosmic rays (GCR). This article considers aspects of radiation track structure in relation to the relative biological effectiveness (RBE) of HZE particles and the quality factor used for space radiation. The NASA quality factor (QFNASA) is composed of two terms, which can be interpreted as broadly representing the low- and the high-ionization-density components of the HZE particle tracks. These are discussed in turn as they relate to available experimental evidence on the biological effectiveness of such components. Also briefly described are subsequent published proposals for a reformulation of the quality factor to relate more directly to the acute -ray exposures from the atomic bombs and for further refinement of the parameter values (and their uncertainties) that determine the shape of the quality factor function. Other recent developments are also mentioned

Effect of microplastic on the gills of the Shore Crab Carcinus maenas

This is a “Just Accepted” manuscript. "Just Accepted manuscripts" have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.Microscopic plastic debris (microplastics, <5mm in diameter) is ubiquitous in the marine environment. Previous work has shown that microplastics may be ingested and inhaled by the shore crab Carcinus maenas although the biological consequences are unknown. Here, we show that acute aqueous exposure to polystyrene microspheres (8μm) with different surface coatings had significant but transient effects on branchial function. Microspheres inhaled into the gill chamber had a small but significant dose dependent effect on oxygen consumption after 1 hour of exposure, returning to normal levels after 16 h. Ion exchange was also affected, with a small but significant decrease in hemolymph sodium ions and an increase in calcium ions after 24 h post exposure. To further asses the effects on osmoregulation, crabs were challenged with reduced salinity after microplastic exposure. Neither microspheres nor natural sediments altered the crab’s response to osmotic stress, regardless of plastic concentration added. Carboxylated (COOH) and aminated (NH2) polystyrene microspheres were distributed differently across the gill surface, although neither had a significant adverse impact on gill function. These results illustrate the extent of the physiological effects of microplastics, compared to the physiological resilience of shore crabs in maintaining osmoregulatory and respiratory function after acute exposure to both anthropogenic plastics and natural particles.W, CL and TG acknowledge funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 308370. The contents of this publication are the responsibility of the CleanSea project and can in no way be taken to reflect the views of the European Union. TG and CL acknowledge additional support from NERC NE/L007010/1

Biological Effects of Stellar Collapse Neutrinos

Massive stars in their final stages of collapse radiate most of their binding energy in the form of MeV neutrinos. The recoil atoms that they produce in elastic scattering off nuclei in organic tissue create radiation damage which is highly effective in the production of irreparable DNA harm, leading to cellular mutation, neoplasia and oncogenesis. Using a conventional model of the galaxy and of the collapse mechanism, the periodicity of nearby stellar collapses and the radiation dose are calculated. The possible contribution of this process to the paleontological record of mass extinctions is examined.Comment: gzipped PostScript (filename.ps.Z), 12 pages. Final version, Phys. Rev. Lett., in pres

Detailed analysis of the cell-inactivation mechanism by accelerated protons and light ions

Published survival data for V79 cells irradiated by monoenergetic protons, helium-3, carbon, and oxygen ions and for CHO cells irradiated by carbon ions have been analyzed using the probabilistic two-stage model of cell inactivation. Three different classes of DNA damages formed by traversing particles have been distinguished, namely severe single-track damages which might lead to cell inactivation directly, less severe damages where cell inactivation is caused by their combinations, and damages of negligible severity that can be repaired easily. Probabilities of single ions to form these damages have been assessed in dependence on their linear energy transfer (LET) values. Damage induction probabilities increase with atomic number and LET. While combined damages play crucial role at lower LET values, single-track damages dominate in high-LET regions. The yields of single-track lethal damages for protons have been compared with the Monte Carlo estimates of complex DNA lesions, indicating that lethal events correlate well with complex DNA double-strand breaks. The decrease in the single-track damage probability for protons of LET above approx. 30 keV/$\mu$m, suggested by limited experimental evidence, is discussed, together with the consequent differences in the mechanisms of biological effects between protons and heavier ions. Applications of the results in hadrontherapy treatment planning are outlined.Comment: submitted to Physics in Medicine and Biolog

Alpha-particle-induced complex chromosome exchanges transmitted through extra-thymic lymphopoiesis in vitro show evidence of emerging genomic instability

Human exposure to high-linear energy transfer α-particles includes environmental (e.g. radon gas and its decay progeny), medical (e.g. radiopharmaceuticals) and occupational (nuclear industry) sources. The associated health risks of α-particle exposure for lung cancer are well documented however the risk estimates for leukaemia remain uncertain. To further our understanding of α-particle effects in target cells for leukaemogenesis and also to seek general markers of individual exposure to α-particles, this study assessed the transmission of chromosomal damage initially-induced in human haemopoietic stem and progenitor cells after exposure to high-LET α-particles. Cells surviving exposure were differentiated into mature T-cells by extra-thymic T-cell differentiation in vitro. Multiplex fluorescence in situ hybridisation (M-FISH) analysis of naïve T-cell populations showed the occurrence of stable (clonal) complex chromosome aberrations consistent with those that are characteristically induced in spherical cells by the traversal of a single α-particle track. Additionally, complex chromosome exchanges were observed in the progeny of irradiated mature T-cell populations. In addition to this, newly arising de novo chromosome aberrations were detected in cells which possessed clonal markers of α-particle exposure and also in cells which did not show any evidence of previous exposure, suggesting ongoing genomic instability in these populations. Our findings support the usefulness and reliability of employing complex chromosome exchanges as indicators of past or ongoing exposure to high-LET radiation and demonstrate the potential applicability to evaluate health risks associated with α-particle exposure.This work was supported by the Department of Health, UK. Contract RRX95 (RMA NSDTG)

A Comprehensive Genetic Analysis of Candidate Genes Regulating Response to Trypanosoma congolense Infection in Mice

Background: African trypanosomes are protozoan parasites that cause "sleeping sickness" in humans and a similar disease in livestock. Trypanosomes also infect laboratory mice and three major quantitative trait loci (QTL) that regulate survival time after infection with T. congolense have been identified in two independent crosses between susceptible A/J and BALB/c mice, and the resistant C57BL/6. These were designated Tir1, Tir2 and Tir3 for Trypanosoma infection response, and range in size from 0.9-12 cM.Principal Findings: Mapping loci regulating survival time after T. congolense infection in an additional cross revealed that susceptible C3H/HeJ mice have alleles that reduce survival time after infection at Tir1 and Tir3 QTL, but not at Tir2. Next-generation resequencing of a 6.2 Mbp region of mouse chromosome 17, which includes Tir1, identified 1,632 common single nucleotide polymorphisms (SNP) including a probably damaging non-synonymous SNP in Pram1 (PML-RAR alpha-regulated adaptor molecule 1), which was the most plausible candidate QTL gene in Tir1. Genome-wide comparative genomic hybridisation identified 12 loci with copy number variants (CNV) that correlate with differential gene expression, including Cd244 (natural killer cell receptor 2B4), which lies close to the peak of Tir3c and has gene expression that correlates with CNV and phenotype, making it a strong candidate QTL gene at this locus.Conclusions: By systematically combining next-generation DNA capture and sequencing, array-based comparative genomic hybridisation (aCGH), gene expression data and SNP annotation we have developed a strategy that can generate a short list of polymorphisms in candidate QTL genes that can be functionally tested.</p

Electron Emission from Foils and Biological Materials after Proton Impact

Electron emission spectra from thin metal foils with thin layers of water frozen on them (amorphous solid water) after fast proton impact have been measured and have been simulated in liquid water using the event-by-event track structure code PARTRAC. The electron transport model of PARTRAC has been extended to simulate electron transport down to 1 eV by including low-energy phonon, vibrational and electronic excitations as measured by Michaud et al. (Radiat. Res. 159, 3–22, 2003) for amorphous ice. Simulated liquid water yields follow in general the amorphous solid water measurements at higher energies, but overestimate them significantly at energies below 50 eV. Originally published Radiation Physics and Chemistry, Vol. 77, No. 10-12, Oct-Dec 200

Studies of the dose-effect relation

Dose-effect relations and, specifically, cell survival curves are surveyed with emphasis on the interplay of the random factors — biological variability, stochastic reaction of the cell, and the statistics of energy deposition —that co-determine their shape. The global parameters mean inactivation dose, , and coefficient of variance, V, represent this interplay better than conventional parameters. Mechanisms such as lesion interaction, misrepair, repair overload, or repair depletion have been invoked to explain sigmoid dose dependencies, but these notions are partly synonymous and are largely undistinguishable on the basis of observed dose dependencies. All dose dependencies reflect, to varying degree, the microdosimetric fluctuations of energy deposition, and these have certain implications, e.g. the linearity of the dose dependence at small doses, that apply regardless of unresolved molecular mechanisms of cellular radiation action